chr4-160952440-C-T

Variant names:

• chr4-160952440-C-T
• rs9308018

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.24 in 151,908 control chromosomes in the GnomAD database, including 4,674 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4674 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36427 AN: 151788 Hom.: 4661 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.213

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.240 AC: 36464 AN: 151908 Hom.: 4674 Cov.: 31 AF XY: 0.244 AC XY: 18076 AN XY: 74186

African (AFR) AF: 0.290 AC: 12005 AN: 41448

American (AMR) AF: 0.265 AC: 4033 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1015 AN: 5144

South Asian (SAS) AF: 0.148 AC: 712 AN: 4818

European-Finnish (FIN) AF: 0.293 AC: 3089 AN: 10530

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14364 AN: 67952

Other (OTH) AF: 0.215 AC: 452 AN: 2102

Alfa AF: 0.212 Hom.: 1801

Bravo AF: 0.239

Asia WGS AF: 0.166 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9308018; hg19: chr4-161873592;